CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		RDfolder
MCC	0.629	>	0.425
Average MCC ± 95% Confidence Intervals	0.603 ± 0.112	>	0.394 ± 0.127
Sensitivity	0.532	>	0.331
Positive Predictive Value	0.752	>	0.558
Total TP	288	>	179
Total TN	47467	<	47529
Total FP	101	<	147
Total FP CONTRA	10	=	10
Total FP INCONS	85	<	132
Total FP COMP	6	>	5
Total FN	253	<	362
P-value	5.1503931209e-08

Comparison of performance of Cylofold and RDfolder. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for Cylofold and RDfolder).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for Cylofold and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for Cylofold and RDfolder. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for Cylofold and RDfolder).

Total Scores
MCC	0.629
Average MCC ± 95% Confidence Intervals	0.603 ± 0.112
Sensitivity	0.532
Positive Predictive Value	0.752
Nr of predictions	21

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2XQD_Y	tRNA links to Rfam database...	0.81	0.78	0.84	21	2825	4	4	0	0	6
3ADB_C	-	0.78	0.71	0.87	27	4155	4	0	4	0	11
3AKZ_H	tRNA links to Rfam database...	0.66	0.57	0.76	16	2680	6	0	5	1	12
3AM1_B	-	0.76	0.63	0.92	22	3216	2	0	2	0	13
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3J0L_a	-	0.22	0.19	0.27	3	1117	8	1	7	0	13
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_7	-	0.30	0.29	0.33	5	1210	10	0	10	0	12
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3NKB_B	-	0.40	0.31	0.53	8	2001	7	0	7	0	18
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.62	0.50	0.78	21	3889	6	0	6	0	21
3W3S_B	tRNA-Sec links to Rfam database...	0.44	0.38	0.52	15	4724	15	0	14	1	25
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ATO_G	-	0.73	0.70	0.78	7	519	2	1	1	0	3
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

Total Scores
MCC	0.425
Average MCC ± 95% Confidence Intervals	0.394 ± 0.127
Sensitivity	0.331
Positive Predictive Value	0.558
Nr of predictions	21

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.88	0.78	1.00	14	847	0	0	0	0	4
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1526	14	2	12	0	20
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3ADB_C	-	0.46	0.39	0.54	15	4158	13	0	13	0	23
3AKZ_H	tRNA links to Rfam database...	0.48	0.43	0.55	12	2679	11	1	9	1	16
3AM1_B	-	0.47	0.43	0.54	15	3212	13	1	12	0	20
3AMU_B	tRNA links to Rfam database...	0.18	0.15	0.22	4	2985	16	2	12	2	23
3J0L_a	-	-0.01	0.00	0.00	0	1124	4	1	3	0	16
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1220	5	0	5	0	17
3J16_L	tRNA links to Rfam database...	0.22	0.17	0.31	5	2759	11	0	11	0	25
3J20_0	tRNA links to Rfam database...	0.73	0.57	0.94	17	2832	2	0	1	1	13
3NKB_B	-	0.37	0.31	0.47	8	1999	9	0	9	0	18
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.30	0.17	0.54	7	3903	6	0	6	0	35
3W3S_B	tRNA-Sec links to Rfam database...	0.27	0.23	0.33	9	4726	18	1	17	0	31
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ATO_G	-	0.63	0.40	1.00	4	524	0	0	0	0	6
4ENB_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1265	4	0	4	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.